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gchandra@loginsiddhi:~/GraphChainer/Human$/nlsasfs/home/dnarna/gchandra/GraphChainer/GraphChainer/bin/GraphChainer -t 128 -f /nlsasfs/home/dnarna/gchandra/BWA/Data/ERR194147_1.fastq.gz -f /nlsasfs/home/dnarna/gchandra/BWA/Data/ERR194147_2.fastq.gz -g /nlsasfs/home/dnarna/gchandra/GraphChainer/Human/Graph/graph.gfa -a out.gam

GraphChainer Branch master commit 403cff6 2022-01-05 10:59:13 +0200
GraphChainer Branch master commit 403cff6 2022-01-05 10:59:13 +0200
Co-linear chaining on splits=(35,35,10000)
Load graph from /nlsasfs/home/dnarna/gchandra/GraphChainer/Human/Graph/graph.gfa
GraphChainer: src/GfaGraph.cpp:231: static GfaGraph GfaGraph::LoadFromStream(std::istream&, bool, bool): Assertion `dummy == "S"' failed.
Aborted (core dumped)

Constructed Graph with;
vg construct -t 128 -a -r Homo_sapiens_assembly38.fasta -v Homo_sapiens_assembly38.known_indels.vcf.gz -p -m 3000000 > graph.gfa

Hello,

would you like to tag a release version ?

regards

Eric

Hello :)

An attempt to run GraphChainer with non-integer --sampling-step parameter raises an error:

the argument ('0.1') for option '--sampling-step' is invalid

which clashes with its description in README.md:

--sampling-step Sampling step factor (default 1). Use >1 (<1, >0) for faster (slower), but less (more) accurate alignments. It increases (decreases) the sampling sparsity of fragments.

I run GraphChainer on a gfa file built using seqwish and a fasta file of reads simulated from one of the genome used to construct the Graph.
I used the command GraphChainer -g graph.gfa -f reads.fa - a alignment.json

I got the following message

GraphChainer Branch master commit c083580a2ca5c9d3772da41d2106d0795de500e6 2022-03-30 09:59:42 +0300
GraphChainer Branch master commit c083580a2ca5c9d3772da41d2106d0795de500e6 2022-03-30 09:59:42 +0300
Co-linear chaining on splits=(35,35,10000)
Load graph from graph.gfa
Build alignment graph
5992064 original nodes, 2996032 in one strand
6131490 split nodes, 3065745 in one strand
0 ambiguous split nodes
21011356 base pairs (total characters), 10505678 in one strand
9087448 edges, 4543724 in one strand
1518594 nodes with in-degree >= 2, 759297 in one strand
Build MPC Index
2 connected components
cid = 0 path #0 : 33195 33195 5950803
cid = 0 path #0 : 33193 16597 5934206
cid = 0 path #0 : 33193 15714 5918492
cid = 0 path #0 : 5125 5125 5913367
cid = 0 path #0 : 5123 2562 5910805
cid = 0 path #0 : 5123 2414 5908391
Signal 11. Read: ��0�4��. Seed: 0+,0,0,0
Aborted

can you help solve this issue?

Hi,

Thanks for this nice contribution to the graph alignment community. I am working on integrating it to one of my pipelines and I get an error on the first run:

Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
Read m64043_200710_174426/70452667/ccs alignment failed (assertion!)

The input GFA looks like this:

There were multiple reads which failed the assertion, so I reran it which just one read and one thread:

GraphChainer -a test_graphchainer.gaf -g graph_no_empty.gfa -f test.fasta --verbose

which resulted in this output:

GraphChainer Branch master commit 3d2273954299ce413a5eaf1ed6eb6596eb3e485a 2023-03-13 18:15:17 +0200
GraphChainer Branch master commit 3d2273954299ce413a5eaf1ed6eb6596eb3e485a 2023-03-13 18:15:17 +0200
Co-linear chaining on splits=(35,35,10000)
Load graph from graph_no_empty.gfa
Build alignment graph
50 original nodes, 25 in one strand
410 split nodes, 205 in one strand
0 ambiguous split nodes
24706 base pairs (total characters), 12353 in one strand
444 edges, 222 in one strand
12 nodes with in-degree >= 2, 6 in one strand
Build MPC Index
2 connected components
cid = 0 path #0 : 181 181 24
cid = 0 path #0 : 8 4 20
cid = 0 path #0 : 8 4 16
cid = 0 path #0 : 8 4 12
cid = 0 path #0 : 8 4 8
cid = 0 path #0 : 2 2 6
cid = 0 path #0 : 2 2 4
cid = 0 path #0 : 2 2 2
cid = 0 path #0 : 2 2 0
cid = 0 greedy width 9
start shrinkink from width 9
cid = 0 optimal width 9
cid = 0 MPC index done
cid = 1 path #0 : 181 181 24
cid = 1 path #0 : 8 4 20
cid = 1 path #0 : 8 4 16
cid = 1 path #0 : 8 4 12
cid = 1 path #0 : 8 4 8
cid = 1 path #0 : 2 2 6
cid = 1 path #0 : 2 2 4
cid = 1 path #0 : 2 2 2
cid = 1 path #0 : 2 2 0
cid = 1 greedy width 9
start shrinkink from width 9
cid = 1 optimal width 9
cid = 1 MPC index done
MPC building done
total width 18 and max component width 9
Build minimizer seeder from the graph
Minimizer seeds, length 15, window size 20, density 10
Seed cluster size 1
Initial bandwidth 10
write alignments to test_graphchainer.gaf
Align
Read m64043_200710_174426/70452667/ccs seeding took 1ms
src/GraphAligner.h:259: Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed. Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
Read m64043_200710_174426/70452667/ccs alignment failed (assertion!)
Trying to align long readm64043_200710_174426/70452667/ccsRead m64043_200710_174426/70452667/ccs alignment failed (assertion!)
src/GraphAligner.h:259: Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed. Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
terminate called after throwing an instance of 'ThreadReadAssertion::AssertionFailure'
Aborted

I have uploaded the GFA and the FASTA here:

https://storage.googleapis.com/rlorigro-public/graphchainer/graph_no_empty.gfa
https://storage.googleapis.com/rlorigro-public/graphchainer/test.fasta

Thanks

i want to map the contig to my graph,but there is error when running this code:
GraphChainer -f contig.fa -g chr16_parm_2.gfa -a chr16Vshap1.gam -t 100

this error shows in blow:
GraphChainer Branch master commit 403cff6 2022-01-05 10:59:13 +0200
GraphChainer Branch master commit 403cff6 2022-01-05 10:59:13 +0200
Co-linear chaining on splits=(35,35,10000)
Load graph from chr16_parm_2.gfa
Build alignment graph
798 original nodes, 399 in one strand
1715331 split nodes, 857665 in one strand
0 ambiguous split nodes
109732932 base pairs (total characters), 54866466 in one strand
1716013 edges, 858006 in one strand
773 nodes with in-degree >= 2, 386 in one strand
Build MPC Index
2 connected components
cid = 0 path #0 : 35295 35295 822364
cid = 0 path #0 : 26911 26911 795453
cid = 0 path #0 : 822 822 794631
cid = 0 path #0 : 821 821 793810
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cid = 0 path #0 : 820 820 792169
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Signal 11. Read: X��W���qe�. Seed: 0+,0,0,0
can you help me? thank~